Hi all,

I have 4 datasets (Brain region A (Control & Disease), Brain region B (Control & Disease)) and performed scRNA-seq by integrating all data.

And I want to compare Disease and Control in each brain region using pseudo-bulk DEG analysis. (ex. Region A Disease vs Region A Control)

Even if area A and area B are integrated, is it ok to perform DEG analysis for each brain region with the code below?

dds <- DESeqDataSetFromMatrix(cluster_counts, 
                            colData = cluster_metadata, 
                            design = ~ group_id)
contrast <- c("group_id", "Region A Disease", "Region A Control")
### or contrast <- c("group_id", "Region B Disease", "Region B Control")
res <- results(dds, 
             contrast = contrast,
             alpha = 0.05)

group_id contains 'Region A Disease', 'Region A Control', 'Region B Disease', and 'Region B Control'.

Or should I do it another way?

Thanks in advance,

Joonhong